GapMind for catabolism of small carbon sources


Definition of 2-deoxy-D-ribose catabolism

As rules and steps, or see full text


Overview: Deoxyribose utilization in GapMind is based on MetaCyc pathways 2-deoxy-D-ribose degradation I via deoxyribose 5-phosphate aldolase (link) and pathway II via oxidation to 2-deoxy-3-dehydro-D-ribonate (link).


deoP: deoxyribose transporter

deoK: deoxyribokinase

deoC: deoxyribose-5-phosphate aldolase

ald-dh-CoA: acetaldehyde dehydrogenase, acylating

adh: acetaldehyde dehydrogenase (not acylating)

acs: acetyl-CoA synthetase, AMP-forming

ackA: acetate kinase

pta: phosphate acetyltransferase

drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit

drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit

drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component

atoA: acetoacetyl-CoA transferase, A subunit

atoD: acetoacetyl-CoA transferase, B subunit

aacS: acetoacetyl-CoA synthetase

atoB: acetyl-CoA C-acetyltransferase

deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase

ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme

garK: glycerate 2-kinase

deoxyribonate-transport: 2-deoxy-D-ribonate transporter



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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory